I just fixed the bug where it always prompts for SQL named instances. I will release the new build later this week. It will probably be v2.3.1.
Regarding the including or excluding the SQL default instances, right now I use a simple InputBox to get the named instances into the export. To have the option of including or exclusing the default instance would require a custom form with an input box for
the named instances and a checkbox to include the default instance or not, or I could just create a separate prompt for it. In any case, how would you prefer it ask about the default instance? Please keep in mind that I am not a professional developer. I know
just enough VB.NET to get by, so please be gentle. :-)

What if your dialog box had a default value of "Default". If users wanted to add named instances they would just say "Default;Instance01;Instance02;" Or if they only wanted named instance they would say "Instance01;Instance02;".
So your program only outputs default instance counters id the keyword Default is there?